Starting phenix.real_space_refine on Wed Mar 20 07:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybl_33725/03_2024/7ybl_33725.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 17018 2.51 5 N 4321 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26819 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.44, per 1000 atoms: 0.50 Number of scatterers: 26819 At special positions: 0 Unit cell: (139.1, 141.24, 197.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5369 8.00 N 4321 7.00 C 17018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 11.41 Conformation dependent library (CDL) restraints added in 4.7 seconds 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 53 sheets defined 26.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.624A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.255A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.291A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.818A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.744A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.954A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.669A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.542A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.164A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.862A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.556A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.317A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.722A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.051A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.819A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.455A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.136A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.790A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.118A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.937A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.528A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.734A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.504A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.098A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.195A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.876A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C1160 " --> pdb=" O PHE C1156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.688A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.623A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121 removed outlier: 12.174A pdb=" N ALA A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N GLU A 169 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.469A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.777A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.508A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.608A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.529A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.935A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.300A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.693A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.580A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.772A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.650A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.317A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.555A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.718A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.523A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.098A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.761A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.343A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.570A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.072A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.878A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.652A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ALA C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 169 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.468A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.717A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.717A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.509A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.687A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 7.131A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 2763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.78 Time building geometry restraints manager: 12.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7523 1.33 - 1.46: 6466 1.46 - 1.58: 13285 1.58 - 1.70: 1 1.70 - 1.83: 138 Bond restraints: 27413 Sorted by residual: bond pdb=" C LEU B 977 " pdb=" N ASN B 978 " ideal model delta sigma weight residual 1.335 1.470 -0.135 1.36e-02 5.41e+03 9.83e+01 bond pdb=" C VAL A 83 " pdb=" N LEU A 84 " ideal model delta sigma weight residual 1.329 1.385 -0.056 1.35e-02 5.49e+03 1.73e+01 bond pdb=" N PRO B 986 " pdb=" CD PRO B 986 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" N PRO C 986 " pdb=" CD PRO C 986 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 27408 not shown) Histogram of bond angle deviations from ideal: 97.66 - 106.02: 686 106.02 - 114.38: 16580 114.38 - 122.73: 17073 122.73 - 131.09: 2896 131.09 - 139.45: 68 Bond angle restraints: 37303 Sorted by residual: angle pdb=" O ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 122.06 99.87 22.19 1.14e+00 7.69e-01 3.79e+02 angle pdb=" O ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 121.87 104.00 17.87 9.70e-01 1.06e+00 3.39e+02 angle pdb=" CA ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 117.15 135.17 -18.02 1.14e+00 7.69e-01 2.50e+02 angle pdb=" CA ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 117.87 136.91 -19.04 1.25e+00 6.40e-01 2.32e+02 angle pdb=" C ILE B 993 " pdb=" N ASP B 994 " pdb=" CA ASP B 994 " ideal model delta sigma weight residual 120.44 136.94 -16.50 1.30e+00 5.92e-01 1.61e+02 ... (remaining 37298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 16661 24.18 - 48.35: 889 48.35 - 72.53: 130 72.53 - 96.70: 72 96.70 - 120.88: 41 Dihedral angle restraints: 17793 sinusoidal: 8373 harmonic: 9420 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 175.82 -82.82 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.08 -81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.90 -74.10 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 17790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4465 0.133 - 0.267: 74 0.267 - 0.400: 4 0.400 - 0.534: 1 0.534 - 0.667: 1 Chirality restraints: 4545 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.04e+01 chirality pdb=" C1 NAG C1403 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1403 " pdb=" O5 NAG C1403 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4542 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.131 5.00e-02 4.00e+02 1.85e-01 5.47e+01 pdb=" N PRO C 986 " 0.319 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO A 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " -0.117 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO C 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.081 5.00e-02 4.00e+02 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 92 2.44 - 3.05: 17738 3.05 - 3.67: 38714 3.67 - 4.28: 56401 4.28 - 4.90: 92422 Nonbonded interactions: 205367 Sorted by model distance: nonbonded pdb=" OD1 ASP B 985 " pdb=" CD PRO B 987 " model vdw 1.819 3.440 nonbonded pdb=" OG SER C 816 " pdb=" CD PRO C 817 " model vdw 2.003 3.440 nonbonded pdb=" OG SER B 816 " pdb=" CD PRO B 817 " model vdw 2.022 3.440 nonbonded pdb=" OD2 ASP B 985 " pdb=" CG PRO B 987 " model vdw 2.039 3.440 nonbonded pdb=" OG SER B 31 " pdb=" OG SER B 60 " model vdw 2.119 2.440 ... (remaining 205362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1162 or resid 1401 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.520 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 71.220 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 27413 Z= 0.381 Angle : 0.960 22.194 37303 Z= 0.580 Chirality : 0.053 0.667 4545 Planarity : 0.009 0.185 4675 Dihedral : 16.195 120.877 11607 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 0.60 % Allowed : 0.78 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3198 helix: 1.20 (0.20), residues: 720 sheet: -0.60 (0.19), residues: 669 loop : -1.49 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.008 0.001 HIS C 49 PHE 0.053 0.002 PHE C 238 TYR 0.035 0.002 TYR A 242 ARG 0.026 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 512 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 THR cc_start: 0.6000 (p) cc_final: 0.5564 (p) REVERT: B 1089 PHE cc_start: 0.7064 (m-80) cc_final: 0.6745 (m-10) REVERT: C 38 TYR cc_start: 0.3668 (m-10) cc_final: 0.3391 (m-80) REVERT: C 380 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: C 1094 VAL cc_start: 0.3715 (p) cc_final: 0.3385 (p) outliers start: 17 outliers final: 5 residues processed: 526 average time/residue: 0.3632 time to fit residues: 302.9414 Evaluate side-chains 257 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 251 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 0.0770 chunk 187 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1118 HIS B 49 HIS B 211 ASN B 388 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1002 GLN B1005 GLN B1058 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 913 GLN C 935 GLN C1054 GLN C1119 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 27413 Z= 0.248 Angle : 0.768 13.781 37303 Z= 0.376 Chirality : 0.049 0.500 4545 Planarity : 0.006 0.068 4675 Dihedral : 12.995 102.747 5779 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 2.19 % Allowed : 8.83 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3198 helix: 1.37 (0.20), residues: 723 sheet: -0.64 (0.19), residues: 714 loop : -1.44 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 104 HIS 0.010 0.001 HIS A1118 PHE 0.033 0.002 PHE A 86 TYR 0.021 0.002 TYR B1067 ARG 0.008 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 306 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.2645 (m-10) cc_final: 0.2212 (m-80) REVERT: A 285 ILE cc_start: 0.4215 (mt) cc_final: 0.4010 (mt) REVERT: A 571 ASP cc_start: 0.5662 (t0) cc_final: 0.5440 (t0) REVERT: B 494 SER cc_start: 0.5475 (OUTLIER) cc_final: 0.5115 (t) REVERT: B 740 MET cc_start: 0.7317 (tpp) cc_final: 0.7113 (tpp) REVERT: B 775 ASP cc_start: 0.6182 (m-30) cc_final: 0.5910 (m-30) REVERT: B 902 MET cc_start: 0.7520 (tpp) cc_final: 0.7213 (tpt) REVERT: B 916 LEU cc_start: 0.5854 (tp) cc_final: 0.5477 (tp) REVERT: C 386 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5877 (ttpt) REVERT: C 906 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6746 (t80) outliers start: 62 outliers final: 34 residues processed: 349 average time/residue: 0.3310 time to fit residues: 192.5744 Evaluate side-chains 264 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 751 ASN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B1002 GLN B1054 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 954 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5821 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27413 Z= 0.217 Angle : 0.701 12.228 37303 Z= 0.336 Chirality : 0.046 0.439 4545 Planarity : 0.005 0.063 4675 Dihedral : 11.357 101.470 5769 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.12 % Allowed : 12.50 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3198 helix: 1.49 (0.20), residues: 741 sheet: -0.53 (0.19), residues: 747 loop : -1.36 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 104 HIS 0.010 0.001 HIS C 49 PHE 0.025 0.002 PHE A 86 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 260 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.3083 (m-10) cc_final: 0.2559 (m-10) REVERT: A 571 ASP cc_start: 0.6000 (t70) cc_final: 0.5665 (t0) REVERT: B 494 SER cc_start: 0.5493 (OUTLIER) cc_final: 0.5153 (t) REVERT: B 740 MET cc_start: 0.7337 (tpp) cc_final: 0.7087 (tpp) REVERT: B 775 ASP cc_start: 0.6669 (m-30) cc_final: 0.6346 (m-30) REVERT: B 902 MET cc_start: 0.7785 (tpp) cc_final: 0.7435 (tpt) REVERT: C 177 MET cc_start: 0.5659 (mpp) cc_final: 0.4650 (ttm) REVERT: C 380 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.4039 (m-80) REVERT: C 916 LEU cc_start: 0.7915 (tp) cc_final: 0.7650 (tp) REVERT: C 1115 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5962 (tp) outliers start: 60 outliers final: 34 residues processed: 301 average time/residue: 0.3366 time to fit residues: 168.3910 Evaluate side-chains 249 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 207 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 655 HIS A 774 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1002 GLN A1083 HIS B1054 GLN C 49 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 27413 Z= 0.298 Angle : 0.788 17.464 37303 Z= 0.380 Chirality : 0.049 0.456 4545 Planarity : 0.005 0.073 4675 Dihedral : 8.867 92.224 5769 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 3.07 % Allowed : 15.25 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3198 helix: 1.18 (0.19), residues: 753 sheet: -0.68 (0.19), residues: 735 loop : -1.53 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 104 HIS 0.012 0.001 HIS C 49 PHE 0.040 0.003 PHE B 106 TYR 0.030 0.002 TYR B 904 ARG 0.013 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 259 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.3524 (m-10) cc_final: 0.2731 (m-10) REVERT: A 388 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6104 (p0) REVERT: A 931 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6544 (mm) REVERT: B 494 SER cc_start: 0.5591 (OUTLIER) cc_final: 0.5264 (t) REVERT: B 740 MET cc_start: 0.7458 (tpp) cc_final: 0.6876 (tpp) REVERT: B 1115 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6524 (tp) REVERT: C 177 MET cc_start: 0.5817 (mpp) cc_final: 0.5501 (mmp) REVERT: C 380 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.4102 (m-80) REVERT: C 714 ILE cc_start: 0.8261 (mm) cc_final: 0.7961 (mm) REVERT: C 902 MET cc_start: 0.8248 (tpp) cc_final: 0.7973 (tpt) REVERT: C 1050 MET cc_start: 0.8470 (ptp) cc_final: 0.8247 (ptt) REVERT: C 1115 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6661 (tp) outliers start: 87 outliers final: 52 residues processed: 328 average time/residue: 0.3551 time to fit residues: 188.9257 Evaluate side-chains 259 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 201 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 214 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 0.0970 chunk 278 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 953 ASN C 81 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 27413 Z= 0.288 Angle : 0.777 15.620 37303 Z= 0.373 Chirality : 0.048 0.437 4545 Planarity : 0.005 0.072 4675 Dihedral : 7.595 76.994 5769 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 3.78 % Allowed : 16.84 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3198 helix: 1.27 (0.19), residues: 753 sheet: -0.73 (0.19), residues: 744 loop : -1.54 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 104 HIS 0.004 0.001 HIS C 66 PHE 0.030 0.002 PHE B 823 TYR 0.023 0.002 TYR B1067 ARG 0.007 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 216 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6356 (p0) REVERT: A 900 MET cc_start: 0.7326 (mmt) cc_final: 0.7011 (mmt) REVERT: B 494 SER cc_start: 0.5718 (OUTLIER) cc_final: 0.5385 (t) REVERT: B 571 ASP cc_start: 0.6065 (t0) cc_final: 0.5812 (t0) REVERT: B 881 THR cc_start: 0.8031 (p) cc_final: 0.7411 (m) REVERT: B 902 MET cc_start: 0.8493 (tpt) cc_final: 0.7853 (tpt) REVERT: C 177 MET cc_start: 0.5906 (mpp) cc_final: 0.5639 (mmp) REVERT: C 380 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.4301 (m-80) REVERT: C 1029 MET cc_start: 0.8800 (tpp) cc_final: 0.8573 (tpp) outliers start: 107 outliers final: 66 residues processed: 301 average time/residue: 0.3590 time to fit residues: 177.0405 Evaluate side-chains 248 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 310 optimal weight: 0.4980 chunk 257 optimal weight: 0.0060 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 895 GLN B 784 GLN B 787 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27413 Z= 0.180 Angle : 0.677 15.817 37303 Z= 0.323 Chirality : 0.046 0.435 4545 Planarity : 0.005 0.062 4675 Dihedral : 6.736 63.637 5769 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.90 % Rotamer: Outliers : 2.65 % Allowed : 18.96 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3198 helix: 1.56 (0.20), residues: 753 sheet: -0.58 (0.19), residues: 738 loop : -1.52 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 104 HIS 0.005 0.001 HIS B1088 PHE 0.021 0.001 PHE A1075 TYR 0.015 0.001 TYR C 265 ARG 0.011 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 198 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.0874 (m-80) cc_final: 0.0597 (m-80) REVERT: B 494 SER cc_start: 0.5637 (OUTLIER) cc_final: 0.5318 (t) REVERT: B 552 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6056 (pt) REVERT: B 881 THR cc_start: 0.7934 (p) cc_final: 0.7173 (m) REVERT: B 1115 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6568 (tp) REVERT: C 177 MET cc_start: 0.5937 (mpp) cc_final: 0.5690 (mmp) REVERT: C 380 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.4279 (m-80) REVERT: C 819 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: C 1011 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8922 (tp40) outliers start: 75 outliers final: 40 residues processed: 257 average time/residue: 0.3464 time to fit residues: 148.0734 Evaluate side-chains 221 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1011 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 309 optimal weight: 0.6980 chunk 193 optimal weight: 0.4980 chunk 188 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27413 Z= 0.190 Angle : 0.667 16.694 37303 Z= 0.317 Chirality : 0.045 0.434 4545 Planarity : 0.004 0.066 4675 Dihedral : 6.151 57.787 5769 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 2.82 % Allowed : 19.03 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3198 helix: 1.65 (0.20), residues: 753 sheet: -0.51 (0.19), residues: 732 loop : -1.47 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 PHE 0.021 0.001 PHE B 238 TYR 0.015 0.001 TYR B1067 ARG 0.016 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 180 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 494 SER cc_start: 0.5648 (OUTLIER) cc_final: 0.5339 (t) REVERT: B 881 THR cc_start: 0.7906 (p) cc_final: 0.7217 (m) REVERT: B 1115 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6630 (tp) REVERT: C 177 MET cc_start: 0.5964 (mpp) cc_final: 0.5714 (mmp) REVERT: C 380 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.4444 (m-80) REVERT: C 819 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7193 (mt-10) outliers start: 80 outliers final: 59 residues processed: 242 average time/residue: 0.3334 time to fit residues: 136.9575 Evaluate side-chains 223 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 160 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 152 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A1011 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27413 Z= 0.193 Angle : 0.659 13.377 37303 Z= 0.317 Chirality : 0.045 0.433 4545 Planarity : 0.005 0.065 4675 Dihedral : 5.778 54.836 5769 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 2.97 % Allowed : 19.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3198 helix: 1.76 (0.20), residues: 753 sheet: -0.41 (0.19), residues: 717 loop : -1.51 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 PHE 0.030 0.001 PHE B 238 TYR 0.016 0.001 TYR B1067 ARG 0.010 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 181 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 VAL cc_start: 0.5783 (OUTLIER) cc_final: 0.5573 (m) REVERT: B 494 SER cc_start: 0.5656 (OUTLIER) cc_final: 0.5360 (t) REVERT: B 619 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6856 (mm-30) REVERT: B 881 THR cc_start: 0.7989 (p) cc_final: 0.7294 (m) REVERT: B 984 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7436 (mm) REVERT: C 177 MET cc_start: 0.5950 (mpp) cc_final: 0.5696 (mmm) REVERT: C 380 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.4587 (m-80) REVERT: C 819 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7292 (mt-10) outliers start: 84 outliers final: 62 residues processed: 248 average time/residue: 0.3417 time to fit residues: 142.4921 Evaluate side-chains 229 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 162 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 226 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 287 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.8214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27413 Z= 0.190 Angle : 0.655 13.070 37303 Z= 0.315 Chirality : 0.045 0.432 4545 Planarity : 0.005 0.065 4675 Dihedral : 5.622 57.135 5769 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 2.72 % Allowed : 19.92 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3198 helix: 1.83 (0.20), residues: 753 sheet: -0.49 (0.19), residues: 741 loop : -1.42 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 104 HIS 0.004 0.001 HIS B1088 PHE 0.037 0.002 PHE B 86 TYR 0.017 0.001 TYR A1138 ARG 0.011 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 181 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8949 (tpp) cc_final: 0.8325 (tpt) REVERT: B 171 VAL cc_start: 0.5779 (OUTLIER) cc_final: 0.5571 (m) REVERT: B 494 SER cc_start: 0.5669 (OUTLIER) cc_final: 0.5365 (t) REVERT: B 552 LEU cc_start: 0.7304 (pt) cc_final: 0.7099 (pt) REVERT: B 619 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 984 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7429 (mm) REVERT: C 177 MET cc_start: 0.5917 (mpp) cc_final: 0.5662 (mmp) REVERT: C 194 PHE cc_start: 0.4207 (OUTLIER) cc_final: 0.3530 (m-10) REVERT: C 380 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: C 819 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7286 (mt-10) outliers start: 77 outliers final: 64 residues processed: 244 average time/residue: 0.3320 time to fit residues: 136.0739 Evaluate side-chains 232 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 162 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 294 optimal weight: 0.6980 chunk 254 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 196 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A1002 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 954 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27413 Z= 0.222 Angle : 0.692 13.370 37303 Z= 0.336 Chirality : 0.046 0.434 4545 Planarity : 0.005 0.064 4675 Dihedral : 5.804 56.501 5769 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 2.68 % Allowed : 19.95 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3198 helix: 1.73 (0.20), residues: 753 sheet: -0.48 (0.19), residues: 714 loop : -1.55 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.017 0.001 HIS B 207 PHE 0.031 0.002 PHE B 643 TYR 0.022 0.001 TYR B 38 ARG 0.022 0.001 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 173 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.1351 (m-80) cc_final: 0.0969 (m-80) REVERT: B 424 LYS cc_start: 0.5665 (pttt) cc_final: 0.4894 (mmtp) REVERT: B 494 SER cc_start: 0.5773 (OUTLIER) cc_final: 0.5498 (t) REVERT: B 619 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6777 (mm-30) REVERT: B 984 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7457 (mm) REVERT: C 177 MET cc_start: 0.5918 (mpp) cc_final: 0.5650 (mmm) REVERT: C 194 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.3207 (m-10) REVERT: C 380 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5182 (m-80) REVERT: C 779 GLN cc_start: 0.7617 (tp40) cc_final: 0.7118 (tt0) REVERT: C 819 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7361 (mt-10) outliers start: 76 outliers final: 56 residues processed: 233 average time/residue: 0.3236 time to fit residues: 127.6613 Evaluate side-chains 216 residues out of total 2835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 234 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.214558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.167290 restraints weight = 50290.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.160632 restraints weight = 57726.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.157577 restraints weight = 39571.854| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.8985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27413 Z= 0.173 Angle : 0.650 13.185 37303 Z= 0.311 Chirality : 0.045 0.428 4545 Planarity : 0.005 0.065 4675 Dihedral : 5.573 57.546 5769 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.26 % Allowed : 20.34 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3198 helix: 1.88 (0.20), residues: 750 sheet: -0.54 (0.19), residues: 729 loop : -1.47 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 104 HIS 0.005 0.001 HIS C1118 PHE 0.029 0.001 PHE A 106 TYR 0.033 0.001 TYR B 674 ARG 0.013 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4604.88 seconds wall clock time: 85 minutes 19.52 seconds (5119.52 seconds total)